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- PDB-1g9o: FIRST PDZ DOMAIN OF THE HUMAN NA+/H+ EXCHANGER REGULATORY FACTOR -

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Basic information

Entry
Database: PDB / ID: 1g9o
TitleFIRST PDZ DOMAIN OF THE HUMAN NA+/H+ EXCHANGER REGULATORY FACTOR
ComponentsNHE-RF
KeywordsSIGNALING PROTEIN / PDZ domain / NHERF / COMPLEX
Function / homology
Function and homology information


renal phosphate ion absorption / regulation of renal phosphate excretion / renal sodium ion transport / type 2 metabotropic glutamate receptor binding / glutathione transport / dopamine receptor binding / cerebrospinal fluid circulation / negative regulation of sodium ion transport / microvillus assembly / bile acid secretion ...renal phosphate ion absorption / regulation of renal phosphate excretion / renal sodium ion transport / type 2 metabotropic glutamate receptor binding / glutathione transport / dopamine receptor binding / cerebrospinal fluid circulation / negative regulation of sodium ion transport / microvillus assembly / bile acid secretion / maintenance of epithelial cell apical/basal polarity / import across plasma membrane / regulation of protein kinase activity / gamma-aminobutyric acid import / stereocilium tip / plasma membrane organization / phospholipase C-activating dopamine receptor signaling pathway / cilium organization / channel activator activity / gland morphogenesis / establishment of Golgi localization / fibroblast migration / intracellular phosphate ion homeostasis / plasma membrane protein complex / establishment of epithelial cell apical/basal polarity / type 3 metabotropic glutamate receptor binding / negative regulation of fibroblast migration / auditory receptor cell stereocilium organization / chloride channel regulator activity / negative regulation of mitotic cell cycle / beta-2 adrenergic receptor binding / negative regulation of platelet-derived growth factor receptor signaling pathway / growth factor receptor binding / nuclear migration / regulation of cell size / renal absorption / microvillus membrane / microvillus / phosphatase binding / transport across blood-brain barrier / positive regulation of intrinsic apoptotic signaling pathway / protein-membrane adaptor activity / ruffle / sperm midpiece / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / endomembrane system / morphogenesis of an epithelium / cell periphery / protein localization to plasma membrane / filopodium / PDZ domain binding / brush border membrane / sensory perception of sound / negative regulation of canonical Wnt signaling pathway / beta-catenin binding / negative regulation of ERK1 and ERK2 cascade / Wnt signaling pathway / adenylate cyclase-activating dopamine receptor signaling pathway / regulation of cell shape / actin cytoskeleton / actin cytoskeleton organization / protein-containing complex assembly / vesicle / apical plasma membrane / signaling receptor binding / negative regulation of cell population proliferation / perinuclear region of cytoplasm / extracellular exosome / identical protein binding / membrane / cytoplasm
Similarity search - Function
EBP50, C-terminal / Na(+)/H(+) exchange regulatory cofactor NHERF-1/2 / EBP50, C-terminal / : / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain ...EBP50, C-terminal / Na(+)/H(+) exchange regulatory cofactor NHERF-1/2 / EBP50, C-terminal / : / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Na(+)/H(+) exchange regulatory cofactor NHE-RF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsKarthikeyan, S. / Leung, T. / Birrane, G. / Webster, G. / Ladias, J.A.A.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Crystal structure of the PDZ1 domain of human Na(+)/H(+) exchanger regulatory factor provides insights into the mechanism of carboxyl-terminal leucine recognition by class I PDZ domains.
Authors: Karthikeyan, S. / Leung, T. / Birrane, G. / Webster, G. / Ladias, J.A.
#1: Journal: J.Biol.Chem. / Year: 1998
Title: NHE-RF, a regulatory cofactor for Na(+)-H+ exchange, is a common interactor for merlin and ERM (MERM) proteins;
Authors: MURTHY, A. / GONZALEZ-AGOSTI, C. / CORDERO, E. / PINNEY, D. / CANDIA, C. / SOLOMON, F. / GUSELLA, J. / RAMESH, V.
#2: Journal: Nat.Struct.Biol. / Year: 1998
Title: Crystal structure of the hCASK PDZ domain reveals the structural basis of class II PDZ domain target recognition
Authors: Daniels, D.L. / Cohen, A.R. / Anderson, J.M. / Brunger, A.T.
#3: Journal: Cell(Cambridge,Mass.) / Year: 1996
Title: Crystal structures of a complexed and peptide-free membrane protein-binding domain:Molecular basis of peptide recognition by PDZ
Authors: Doyle, D.A. / Lee, A. / Lewis, J. / Kim, E. / Sheng, M. / MacKinnon, R.
#4: Journal: Nature / Year: 1996
Title: Crystal structure of a PDZ domain
Authors: Morais Cabral, J.H. / Petosa, C. / Sutcliffe, M.J. / Raza, S. / Byron, O. / Poy, F. / Marfatia, S.M. / Chishti, A.H. / Liddington, R.C.
History
DepositionNov 26, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NHE-RF


Theoretical massNumber of molelcules
Total (without water)10,0441
Polymers10,0441
Non-polymers00
Water2,594144
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.568, 51.568, 58.947
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein NHE-RF


Mass: 10043.504 Da / Num. of mol.: 1 / Fragment: PDZ1 DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NHERF / Plasmid: PGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O14745
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: potassium sodium tartrate, sodium citrate, ammonium sulfate, manganese chloride, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
20.05 Mpotassium sodium tartrate1reservoir
30.06 Msodium citrate1reservoir
42 Mammonium sulfate1reservoir
520 mM1reservoirMnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.98401 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 20, 2000 / Details: DUAL SLITS
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98401 Å / Relative weight: 1
ReflectionResolution: 1.5→36 Å / Num. all: 14916 / Num. obs: 14916 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 3.9 / Net I/σ(I): 35
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 10.3 / Num. unique all: 1449 / Rsym value: 15.2 / % possible all: 98.9
Reflection
*PLUS
Num. measured all: 246628
Reflection shell
*PLUS
% possible obs: 98.9 %

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.5→24.6 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.201 1500 10 %RANDOM
Rwork0.181 ---
all0.186 14816 --
obs0.186 14816 98.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.19 Å2 / ksol: 0.4078 e/Å3
Displacement parametersBiso mean: 16.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20.21 Å20 Å2
2--0.23 Å20 Å2
3----0.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.08 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.5→24.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms707 0 0 144 851
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_improper_angle_d1.08
X-RAY DIFFRACTIONc_mcbond_it0.821.5
X-RAY DIFFRACTIONc_mcangle_it1.372
X-RAY DIFFRACTIONc_scbond_it1.212
X-RAY DIFFRACTIONc_scangle_it1.812.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.232 236 9.9 %
Rwork0.189 2154 -
obs-2154 98 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN_REP.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 16.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.08
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.232 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.189

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